Starting phenix.real_space_refine on Sun May 12 19:33:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj6_38394/05_2024/8xj6_38394_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj6_38394/05_2024/8xj6_38394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj6_38394/05_2024/8xj6_38394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj6_38394/05_2024/8xj6_38394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj6_38394/05_2024/8xj6_38394_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj6_38394/05_2024/8xj6_38394_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 S 122 5.16 5 C 14382 2.51 5 N 3858 2.21 5 O 4309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "E PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 22688 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2889 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2865 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2938 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 4752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4752 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 565} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3682 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 438} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 5386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5386 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 647} Chain breaks: 4 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AN2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'AN2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'AN2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13845 SG CYS E 282 71.858 81.459 27.239 1.00151.93 S ATOM 13864 SG CYS E 285 73.663 79.507 24.847 1.00144.96 S ATOM 14094 SG CYS E 314 69.410 77.973 25.486 1.00136.23 S ATOM 19279 SG CYS F 282 80.179 51.549 34.595 1.00154.58 S ATOM 19298 SG CYS F 285 78.301 49.151 33.105 1.00151.86 S ATOM 19510 SG CYS F 314 78.634 53.135 32.549 1.00142.69 S Time building chain proxies: 11.91, per 1000 atoms: 0.52 Number of scatterers: 22688 At special positions: 0 Unit cell: (128.199, 132.508, 156.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 122 16.00 P 15 15.00 O 4309 8.00 N 3858 7.00 C 14382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.73 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 802 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 285 " pdb="ZN ZN E 802 " - pdb=" ND1 HIS E 290 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 314 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 282 " pdb=" ZN F 802 " pdb="ZN ZN F 802 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 802 " - pdb=" SG CYS F 314 " pdb="ZN ZN F 802 " - pdb=" SG CYS F 282 " Number of angles added : 3 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 34 sheets defined 35.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.617A pdb=" N ILE A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.012A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 477 through 489 removed outlier: 4.054A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 7.818A pdb=" N ASP A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.588A pdb=" N THR A 533 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.943A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 removed outlier: 3.979A pdb=" N ARG A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 620' Processing helix chain 'A' and resid 634 through 640 removed outlier: 4.510A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 638 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 4.086A pdb=" N ASP A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 660 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 4.080A pdb=" N LEU A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 702 removed outlier: 4.032A pdb=" N PHE A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.574A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 374 removed outlier: 4.846A pdb=" N HIS B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 386 through 399 Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 456 through 468 removed outlier: 4.351A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 removed outlier: 4.233A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 7.356A pdb=" N ASP B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.594A pdb=" N THR B 533 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 615 through 618 No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.822A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 Processing helix chain 'C' and resid 364 through 374 removed outlier: 4.832A pdb=" N HIS C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 380 No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 431 through 434 No H-bonds generated for 'chain 'C' and resid 431 through 434' Processing helix chain 'C' and resid 456 through 468 removed outlier: 4.189A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 489 removed outlier: 3.660A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 7.340A pdb=" N ASP C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 533 No H-bonds generated for 'chain 'C' and resid 530 through 533' Processing helix chain 'C' and resid 542 through 545 No H-bonds generated for 'chain 'C' and resid 542 through 545' Processing helix chain 'C' and resid 572 through 578 Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.767A pdb=" N LEU C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 695 through 697 No H-bonds generated for 'chain 'C' and resid 695 through 697' Processing helix chain 'D' and resid 3 through 6 No H-bonds generated for 'chain 'D' and resid 3 through 6' Processing helix chain 'D' and resid 21 through 25 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 79 through 103 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.933A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 No H-bonds generated for 'chain 'D' and resid 164 through 167' Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.659A pdb=" N ARG D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 386 through 399 Processing helix chain 'D' and resid 431 through 434 No H-bonds generated for 'chain 'D' and resid 431 through 434' Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 477 through 490 removed outlier: 4.018A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 7.574A pdb=" N ASP D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.674A pdb=" N THR D 533 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 545 No H-bonds generated for 'chain 'D' and resid 542 through 545' Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 637 through 639 No H-bonds generated for 'chain 'D' and resid 637 through 639' Processing helix chain 'D' and resid 654 through 659 Processing helix chain 'D' and resid 665 through 679 removed outlier: 3.617A pdb=" N LEU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 694 through 696 No H-bonds generated for 'chain 'D' and resid 694 through 696' Processing helix chain 'E' and resid 243 through 253 Processing helix chain 'E' and resid 261 through 263 No H-bonds generated for 'chain 'E' and resid 261 through 263' Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 364 through 374 removed outlier: 4.691A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 386 through 399 Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 477 through 489 removed outlier: 4.034A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 523 removed outlier: 7.395A pdb=" N ASP E 522 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU E 523 " --> pdb=" O ALA E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 533 No H-bonds generated for 'chain 'E' and resid 530 through 533' Processing helix chain 'E' and resid 542 through 545 No H-bonds generated for 'chain 'E' and resid 542 through 545' Processing helix chain 'E' and resid 572 through 578 removed outlier: 3.918A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 619 No H-bonds generated for 'chain 'E' and resid 617 through 619' Processing helix chain 'E' and resid 636 through 640 Processing helix chain 'E' and resid 655 through 660 Processing helix chain 'E' and resid 665 through 679 removed outlier: 3.587A pdb=" N LEU E 669 " --> pdb=" O ARG E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 702 removed outlier: 3.887A pdb=" N PHE E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 removed outlier: 3.603A pdb=" N ASN F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 46 Processing helix chain 'F' and resid 79 through 103 Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 144 through 160 removed outlier: 4.231A pdb=" N ARG F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 removed outlier: 3.906A pdb=" N SER F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 164 through 168' Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 243 through 253 Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.683A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 374 removed outlier: 4.565A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.708A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 468 removed outlier: 4.609A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 489 removed outlier: 3.852A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 523 removed outlier: 7.497A pdb=" N ASP F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU F 523 " --> pdb=" O ALA F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.863A pdb=" N THR F 533 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 547 removed outlier: 4.694A pdb=" N MET F 547 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 578 Processing helix chain 'F' and resid 636 through 640 Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 665 through 679 removed outlier: 3.677A pdb=" N LEU F 669 " --> pdb=" O ARG F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 702 Processing sheet with id= A, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= B, first strand: chain 'A' and resid 412 through 414 Processing sheet with id= C, first strand: chain 'A' and resid 621 through 625 removed outlier: 6.290A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 499 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 602 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 501 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 604 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.241A pdb=" N LYS A 647 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER A 631 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS A 649 " --> pdb=" O SER A 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= F, first strand: chain 'B' and resid 412 through 415 Processing sheet with id= G, first strand: chain 'B' and resid 621 through 625 removed outlier: 6.261A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR B 499 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 602 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.381A pdb=" N LYS B 647 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 631 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 649 " --> pdb=" O SER B 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 339 through 341 Processing sheet with id= J, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.663A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 621 through 626 removed outlier: 6.573A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 499 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 602 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= M, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.762A pdb=" N LYS C 647 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER C 631 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LYS C 649 " --> pdb=" O SER C 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.868A pdb=" N PHE D 12 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 64 through 66 removed outlier: 6.356A pdb=" N TYR D 219 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N THR D 143 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N PHE D 221 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 68 through 73 Processing sheet with id= Q, first strand: chain 'D' and resid 339 through 341 Processing sheet with id= R, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.635A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 621 through 626 removed outlier: 6.259A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 600 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE D 501 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE D 602 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY D 503 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR D 604 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 628 through 631 removed outlier: 6.336A pdb=" N LYS D 647 " --> pdb=" O HIS D 629 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER D 631 " --> pdb=" O LYS D 647 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS D 649 " --> pdb=" O SER D 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 294 through 299 Processing sheet with id= V, first strand: chain 'E' and resid 339 through 341 Processing sheet with id= W, first strand: chain 'E' and resid 412 through 414 Processing sheet with id= X, first strand: chain 'E' and resid 621 through 626 removed outlier: 6.054A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE E 600 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE E 501 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 602 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY E 503 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR E 604 " --> pdb=" O GLY E 503 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 581 through 583 Processing sheet with id= Z, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.624A pdb=" N LYS E 647 " --> pdb=" O HIS E 629 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N SER E 631 " --> pdb=" O LYS E 647 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS E 649 " --> pdb=" O SER E 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 32 through 36 removed outlier: 4.120A pdb=" N PHE F 12 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.615A pdb=" N HIS F 134 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE F 67 " --> pdb=" O PHE F 137 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ASP F 139 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N VAL F 65 " --> pdb=" O ASP F 139 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.533A pdb=" N TYR F 219 " --> pdb=" O TYR F 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 294 through 298 Processing sheet with id= AE, first strand: chain 'F' and resid 339 through 341 Processing sheet with id= AF, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.698A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 621 through 626 removed outlier: 6.315A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.377A pdb=" N LYS F 647 " --> pdb=" O HIS F 629 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER F 631 " --> pdb=" O LYS F 647 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS F 649 " --> pdb=" O SER F 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH 622 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 9.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6725 1.33 - 1.45: 3325 1.45 - 1.57: 12886 1.57 - 1.69: 27 1.69 - 1.81: 177 Bond restraints: 23140 Sorted by residual: bond pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 1.795 1.594 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.599 0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 1.795 1.600 0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" N3B AN2 B 801 " pdb=" PB AN2 B 801 " ideal model delta sigma weight residual 1.701 1.586 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" N3B AN2 E 801 " pdb=" PB AN2 E 801 " ideal model delta sigma weight residual 1.701 1.588 0.113 2.00e-02 2.50e+03 3.18e+01 ... (remaining 23135 not shown) Histogram of bond angle deviations from ideal: 97.90 - 106.29: 603 106.29 - 114.69: 13951 114.69 - 123.08: 15367 123.08 - 131.47: 1355 131.47 - 139.87: 39 Bond angle restraints: 31315 Sorted by residual: angle pdb=" C LEU E 321 " pdb=" N ASP E 322 " pdb=" CA ASP E 322 " ideal model delta sigma weight residual 122.94 114.81 8.13 1.50e+00 4.44e-01 2.94e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 139.87 -12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" PA AN2 F 801 " pdb=" O3A AN2 F 801 " pdb=" PB AN2 F 801 " ideal model delta sigma weight residual 123.73 136.64 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" PA AN2 B 801 " pdb=" O3A AN2 B 801 " pdb=" PB AN2 B 801 " ideal model delta sigma weight residual 123.73 136.64 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 139.83 -12.88 3.00e+00 1.11e-01 1.84e+01 ... (remaining 31310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 13879 32.74 - 65.48: 252 65.48 - 98.22: 68 98.22 - 130.96: 1 130.96 - 163.69: 3 Dihedral angle restraints: 14203 sinusoidal: 5929 harmonic: 8274 Sorted by residual: dihedral pdb=" CA GLU E 579 " pdb=" C GLU E 579 " pdb=" N PRO E 580 " pdb=" CA PRO E 580 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ARG A 570 " pdb=" C ARG A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -128.54 163.69 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 14200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2831 0.054 - 0.109: 610 0.109 - 0.163: 85 0.163 - 0.218: 10 0.218 - 0.272: 4 Chirality restraints: 3540 Sorted by residual: chirality pdb=" C3' ANP D 801 " pdb=" C2' ANP D 801 " pdb=" C4' ANP D 801 " pdb=" O3' ANP D 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP C 801 " pdb=" C2' ANP C 801 " pdb=" C4' ANP C 801 " pdb=" O3' ANP C 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3537 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 558 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO F 559 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 559 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 559 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 455 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO D 456 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 456 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 456 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 578 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C THR B 578 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 578 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 579 " -0.014 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1822 2.74 - 3.28: 23939 3.28 - 3.82: 37605 3.82 - 4.36: 46848 4.36 - 4.90: 76070 Nonbonded interactions: 186284 Sorted by model distance: nonbonded pdb=" OG1 THR B 507 " pdb=" O2B AN2 B 801 " model vdw 2.196 2.440 nonbonded pdb=" O GLN D 469 " pdb=" NH1 ARG D 479 " model vdw 2.209 2.520 nonbonded pdb=" O GLY F 508 " pdb=" OG1 THR F 511 " model vdw 2.219 2.440 nonbonded pdb=" NH2 ARG F 514 " pdb=" OE1 GLN F 660 " model vdw 2.222 2.520 nonbonded pdb=" O SER B 455 " pdb=" N MET B 458 " model vdw 2.223 2.520 ... (remaining 186279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 325 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 359 or (resid 360 \ through 361 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 2 through 404 or (resid 405 and (name N or name CA or name C or name O or name C \ B )) or resid 406 through 659 or (resid 660 and (name N or name CA or name C or \ name O or name CB )) or resid 661 through 695)) selection = (chain 'B' and (resid 325 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 404 or (resid 405 \ and (name N or name CA or name C or name O or name CB )) or resid 406 through 53 \ 4 or resid 542 through 561 or resid 566 through 582 or resid 593 through 695)) selection = (chain 'C' and (resid 325 through 343 or (resid 344 and (name N or name CA or na \ me C or name O or name CB )) or resid 345 through 534 or resid 542 through 561 o \ r resid 566 through 582 or resid 593 through 659 or (resid 660 and (name N or na \ me CA or name C or name O or name CB )) or resid 661 through 695)) } ncs_group { reference = (chain 'D' and (resid 5 through 583 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 697 or (resid 69 \ 8 through 700 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 5 through 226 or resid 324 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 534 or \ resid 541 through 700)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.050 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 63.620 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 23140 Z= 0.350 Angle : 0.748 12.917 31315 Z= 0.400 Chirality : 0.046 0.272 3540 Planarity : 0.005 0.083 3983 Dihedral : 14.554 163.694 8809 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.66 % Favored : 95.84 % Rotamer: Outliers : 0.40 % Allowed : 0.48 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2763 helix: 0.02 (0.17), residues: 971 sheet: 0.16 (0.26), residues: 443 loop : -0.28 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 675 HIS 0.011 0.001 HIS A 548 PHE 0.036 0.002 PHE F 554 TYR 0.018 0.001 TYR B 482 ARG 0.011 0.001 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 308 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8217 (pp20) cc_final: 0.7884 (pp20) REVERT: A 426 MET cc_start: 0.7926 (mmp) cc_final: 0.7616 (mmm) REVERT: A 599 THR cc_start: 0.8316 (m) cc_final: 0.7782 (p) REVERT: B 463 ASN cc_start: 0.8390 (m-40) cc_final: 0.8132 (m-40) REVERT: B 513 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7889 (tptp) REVERT: B 514 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7803 (mtm110) REVERT: B 675 TRP cc_start: 0.8236 (m-10) cc_final: 0.8024 (m-10) REVERT: C 458 MET cc_start: 0.8023 (tmm) cc_final: 0.7695 (tmm) REVERT: C 480 GLU cc_start: 0.7881 (pt0) cc_final: 0.7661 (pp20) REVERT: C 596 ASN cc_start: 0.8155 (t0) cc_final: 0.7560 (m-40) REVERT: D 463 ASN cc_start: 0.9255 (m110) cc_final: 0.9026 (m110) REVERT: D 517 LYS cc_start: 0.8967 (pttp) cc_final: 0.8724 (pttp) REVERT: D 675 TRP cc_start: 0.7937 (m-10) cc_final: 0.7393 (m-10) REVERT: E 399 MET cc_start: 0.8316 (mtm) cc_final: 0.8116 (mtp) REVERT: E 491 CYS cc_start: 0.7060 (p) cc_final: 0.6736 (p) REVERT: E 576 LYS cc_start: 0.8562 (tppt) cc_final: 0.8337 (tppt) REVERT: E 696 PHE cc_start: 0.6220 (m-10) cc_final: 0.5820 (m-80) REVERT: F 89 PHE cc_start: 0.8907 (t80) cc_final: 0.8555 (t80) REVERT: F 99 ARG cc_start: 0.8859 (tpm170) cc_final: 0.8530 (tpm170) REVERT: F 133 PHE cc_start: 0.7167 (m-80) cc_final: 0.6899 (m-80) REVERT: F 197 MET cc_start: 0.4484 (mmm) cc_final: 0.4177 (mmm) REVERT: F 300 ASN cc_start: 0.8356 (p0) cc_final: 0.8017 (t0) REVERT: F 369 LEU cc_start: 0.7938 (mm) cc_final: 0.7650 (mt) REVERT: F 471 LEU cc_start: 0.7738 (mt) cc_final: 0.7451 (tp) outliers start: 10 outliers final: 4 residues processed: 317 average time/residue: 0.3733 time to fit residues: 182.1536 Evaluate side-chains 227 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain F residue 45 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 352 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 463 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23140 Z= 0.223 Angle : 0.556 8.129 31315 Z= 0.284 Chirality : 0.043 0.158 3540 Planarity : 0.004 0.053 3983 Dihedral : 10.096 152.714 3224 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.18 % Favored : 96.38 % Rotamer: Outliers : 0.91 % Allowed : 7.53 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2763 helix: 0.27 (0.17), residues: 976 sheet: 0.12 (0.26), residues: 420 loop : -0.30 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 675 HIS 0.004 0.001 HIS F 548 PHE 0.023 0.001 PHE A 357 TYR 0.020 0.001 TYR B 482 ARG 0.005 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8222 (pp20) cc_final: 0.7953 (pp20) REVERT: A 426 MET cc_start: 0.7885 (mmp) cc_final: 0.7599 (mmm) REVERT: A 599 THR cc_start: 0.8242 (m) cc_final: 0.7734 (p) REVERT: B 463 ASN cc_start: 0.8454 (m-40) cc_final: 0.8208 (m-40) REVERT: C 458 MET cc_start: 0.8127 (tmm) cc_final: 0.7878 (tmm) REVERT: C 596 ASN cc_start: 0.8075 (t0) cc_final: 0.7721 (m-40) REVERT: D 152 ARG cc_start: 0.8137 (tpt-90) cc_final: 0.7659 (tpp-160) REVERT: D 156 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7251 (mp0) REVERT: D 214 MET cc_start: 0.7644 (mtp) cc_final: 0.7336 (mtm) REVERT: D 463 ASN cc_start: 0.9292 (m110) cc_final: 0.9066 (m110) REVERT: D 554 PHE cc_start: 0.6824 (t80) cc_final: 0.6350 (t80) REVERT: D 675 TRP cc_start: 0.7960 (m-10) cc_final: 0.7276 (m-10) REVERT: E 399 MET cc_start: 0.8527 (mtm) cc_final: 0.8290 (mtp) REVERT: E 462 MET cc_start: 0.8020 (mpp) cc_final: 0.7800 (mpp) REVERT: E 576 LYS cc_start: 0.8382 (tppt) cc_final: 0.8051 (tppt) REVERT: F 89 PHE cc_start: 0.8916 (t80) cc_final: 0.8635 (t80) REVERT: F 133 PHE cc_start: 0.7363 (m-80) cc_final: 0.6901 (m-80) REVERT: F 369 LEU cc_start: 0.8061 (mm) cc_final: 0.7370 (mt) REVERT: F 471 LEU cc_start: 0.7803 (mt) cc_final: 0.7535 (tp) outliers start: 23 outliers final: 15 residues processed: 263 average time/residue: 0.3474 time to fit residues: 145.3613 Evaluate side-chains 236 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 139 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 209 optimal weight: 0.1980 chunk 171 optimal weight: 7.9990 chunk 69 optimal weight: 0.0970 chunk 251 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 overall best weight: 2.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23140 Z= 0.291 Angle : 0.569 9.105 31315 Z= 0.291 Chirality : 0.043 0.149 3540 Planarity : 0.004 0.053 3983 Dihedral : 9.289 151.925 3218 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.27 % Favored : 95.33 % Rotamer: Outliers : 1.55 % Allowed : 10.06 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2763 helix: 0.26 (0.17), residues: 979 sheet: 0.05 (0.26), residues: 427 loop : -0.35 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 350 HIS 0.009 0.001 HIS C 548 PHE 0.021 0.001 PHE A 357 TYR 0.017 0.001 TYR B 482 ARG 0.007 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8028 (mmp) cc_final: 0.7740 (mmm) REVERT: B 463 ASN cc_start: 0.8462 (m-40) cc_final: 0.8239 (m-40) REVERT: C 458 MET cc_start: 0.8059 (tmm) cc_final: 0.7848 (tmm) REVERT: C 480 GLU cc_start: 0.8141 (pt0) cc_final: 0.7637 (pp20) REVERT: D 78 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7984 (p0) REVERT: D 214 MET cc_start: 0.7642 (mtp) cc_final: 0.7307 (mtm) REVERT: D 554 PHE cc_start: 0.6797 (t80) cc_final: 0.6267 (t80) REVERT: D 675 TRP cc_start: 0.7969 (m-10) cc_final: 0.7373 (m-10) REVERT: E 576 LYS cc_start: 0.8449 (tppt) cc_final: 0.8041 (tppt) REVERT: E 684 MET cc_start: 0.7646 (tmm) cc_final: 0.7273 (tmm) REVERT: F 89 PHE cc_start: 0.8960 (t80) cc_final: 0.8677 (t80) REVERT: F 133 PHE cc_start: 0.7339 (m-80) cc_final: 0.6734 (m-80) REVERT: F 300 ASN cc_start: 0.8246 (p0) cc_final: 0.7980 (t0) REVERT: F 369 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.7732 (tp) REVERT: F 471 LEU cc_start: 0.7872 (mt) cc_final: 0.7643 (tp) outliers start: 39 outliers final: 29 residues processed: 259 average time/residue: 0.3159 time to fit residues: 133.1727 Evaluate side-chains 237 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 248 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 127 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23140 Z= 0.245 Angle : 0.540 7.383 31315 Z= 0.277 Chirality : 0.042 0.146 3540 Planarity : 0.004 0.055 3983 Dihedral : 9.101 151.339 3217 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.91 % Favored : 95.69 % Rotamer: Outliers : 1.86 % Allowed : 11.81 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2763 helix: 0.34 (0.17), residues: 983 sheet: 0.09 (0.26), residues: 412 loop : -0.41 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.007 0.001 HIS C 548 PHE 0.021 0.001 PHE A 357 TYR 0.020 0.001 TYR F 606 ARG 0.005 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 463 ASN cc_start: 0.8355 (m-40) cc_final: 0.8119 (m-40) REVERT: B 513 LYS cc_start: 0.8338 (tmtt) cc_final: 0.8109 (tptp) REVERT: C 480 GLU cc_start: 0.8083 (pt0) cc_final: 0.7694 (pp20) REVERT: C 596 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8014 (m-40) REVERT: D 1 MET cc_start: 0.6132 (tpp) cc_final: 0.5866 (tpp) REVERT: D 78 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7991 (p0) REVERT: D 214 MET cc_start: 0.7664 (mtp) cc_final: 0.7207 (mtm) REVERT: D 554 PHE cc_start: 0.6729 (t80) cc_final: 0.6226 (t80) REVERT: E 447 ASP cc_start: 0.7670 (t0) cc_final: 0.7373 (m-30) REVERT: E 462 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7805 (mpp) REVERT: E 576 LYS cc_start: 0.8464 (tppt) cc_final: 0.8005 (tppt) REVERT: F 89 PHE cc_start: 0.8974 (t80) cc_final: 0.8721 (t80) REVERT: F 133 PHE cc_start: 0.7458 (m-80) cc_final: 0.6849 (m-80) REVERT: F 369 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7582 (mt) outliers start: 47 outliers final: 30 residues processed: 255 average time/residue: 0.3373 time to fit residues: 138.5691 Evaluate side-chains 235 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 222 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 185 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN C 632 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 23140 Z= 0.500 Angle : 0.709 10.846 31315 Z= 0.362 Chirality : 0.047 0.218 3540 Planarity : 0.005 0.054 3983 Dihedral : 9.530 159.090 3215 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.47 % Favored : 94.14 % Rotamer: Outliers : 2.73 % Allowed : 13.15 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2763 helix: -0.15 (0.16), residues: 986 sheet: -0.23 (0.25), residues: 421 loop : -0.67 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 350 HIS 0.012 0.002 HIS C 548 PHE 0.029 0.002 PHE E 668 TYR 0.028 0.002 TYR A 679 ARG 0.008 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 205 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.7007 (ppp) cc_final: 0.6532 (ppp) REVERT: B 463 ASN cc_start: 0.8439 (m-40) cc_final: 0.8222 (m-40) REVERT: C 480 GLU cc_start: 0.8303 (pt0) cc_final: 0.7966 (pp20) REVERT: C 557 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 596 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8210 (t0) REVERT: D 78 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8102 (p0) REVERT: D 214 MET cc_start: 0.7507 (mtp) cc_final: 0.7193 (mtm) REVERT: D 216 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8534 (p0) REVERT: D 554 PHE cc_start: 0.6868 (t80) cc_final: 0.6246 (t80) REVERT: E 369 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8577 (tp) REVERT: E 462 MET cc_start: 0.8116 (mpp) cc_final: 0.7740 (mpp) REVERT: E 684 MET cc_start: 0.7786 (tmm) cc_final: 0.7524 (ttp) REVERT: F 42 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7721 (tmm160) REVERT: F 89 PHE cc_start: 0.8948 (t80) cc_final: 0.8697 (t80) outliers start: 69 outliers final: 43 residues processed: 261 average time/residue: 0.3173 time to fit residues: 136.2150 Evaluate side-chains 239 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 192 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 593 ASN Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 655 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 90 optimal weight: 0.0970 chunk 241 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 268 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN C 632 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23140 Z= 0.193 Angle : 0.545 11.556 31315 Z= 0.276 Chirality : 0.042 0.198 3540 Planarity : 0.004 0.058 3983 Dihedral : 8.879 159.040 3215 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.55 % Favored : 96.06 % Rotamer: Outliers : 2.14 % Allowed : 14.30 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2763 helix: 0.32 (0.17), residues: 991 sheet: -0.21 (0.25), residues: 422 loop : -0.56 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 350 HIS 0.012 0.001 HIS C 548 PHE 0.022 0.001 PHE A 357 TYR 0.014 0.001 TYR A 482 ARG 0.004 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 216 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.7504 (pm20) cc_final: 0.6981 (mm-40) REVERT: B 365 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8859 (m) REVERT: B 369 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8921 (tt) REVERT: B 513 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8190 (tptp) REVERT: C 458 MET cc_start: 0.7959 (tmm) cc_final: 0.7667 (tmm) REVERT: C 480 GLU cc_start: 0.8150 (pt0) cc_final: 0.7843 (pp20) REVERT: D 78 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8062 (p0) REVERT: D 197 MET cc_start: 0.8271 (mtp) cc_final: 0.8046 (mtp) REVERT: D 214 MET cc_start: 0.7449 (mtp) cc_final: 0.7027 (mtm) REVERT: D 554 PHE cc_start: 0.6954 (t80) cc_final: 0.6475 (t80) REVERT: D 684 MET cc_start: 0.7983 (tmm) cc_final: 0.7700 (tmm) REVERT: E 294 HIS cc_start: 0.7107 (m-70) cc_final: 0.6906 (m-70) REVERT: E 462 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7879 (mpp) REVERT: F 42 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7777 (tmm160) REVERT: F 133 PHE cc_start: 0.7502 (m-80) cc_final: 0.6871 (m-80) REVERT: F 240 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7050 (p90) REVERT: F 481 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7785 (tt) outliers start: 54 outliers final: 35 residues processed: 261 average time/residue: 0.3170 time to fit residues: 135.7990 Evaluate side-chains 245 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 258 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 152 optimal weight: 30.0000 chunk 195 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 23140 Z= 0.664 Angle : 0.795 10.165 31315 Z= 0.406 Chirality : 0.050 0.164 3540 Planarity : 0.005 0.057 3983 Dihedral : 9.589 168.372 3215 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.48 % Favored : 93.16 % Rotamer: Outliers : 3.01 % Allowed : 14.86 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2763 helix: -0.35 (0.16), residues: 985 sheet: -0.45 (0.24), residues: 431 loop : -0.85 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 236 HIS 0.010 0.002 HIS C 548 PHE 0.031 0.003 PHE E 668 TYR 0.032 0.002 TYR A 679 ARG 0.008 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 194 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 369 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9115 (tt) REVERT: B 548 HIS cc_start: 0.8989 (p-80) cc_final: 0.8781 (p-80) REVERT: C 458 MET cc_start: 0.7902 (tmm) cc_final: 0.7436 (tmm) REVERT: C 480 GLU cc_start: 0.8422 (pt0) cc_final: 0.8101 (pp20) REVERT: C 614 ASP cc_start: 0.8241 (p0) cc_final: 0.8002 (p0) REVERT: D 1 MET cc_start: 0.6787 (tpp) cc_final: 0.6579 (tpp) REVERT: D 78 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8173 (p0) REVERT: D 214 MET cc_start: 0.7424 (mtp) cc_final: 0.7090 (mtm) REVERT: D 554 PHE cc_start: 0.7205 (t80) cc_final: 0.6776 (t80) REVERT: E 462 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7890 (mpp) REVERT: E 554 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7767 (t80) REVERT: F 42 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7701 (tmm160) REVERT: F 240 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7388 (p90) REVERT: F 369 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8786 (tp) REVERT: F 375 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9314 (tt) REVERT: F 481 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7866 (tt) REVERT: F 655 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6494 (mp) outliers start: 76 outliers final: 51 residues processed: 262 average time/residue: 0.3236 time to fit residues: 136.8925 Evaluate side-chains 241 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 593 ASN Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 655 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 165 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23140 Z= 0.306 Angle : 0.603 11.154 31315 Z= 0.308 Chirality : 0.044 0.169 3540 Planarity : 0.004 0.057 3983 Dihedral : 8.981 166.973 3213 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.56 % Favored : 95.11 % Rotamer: Outliers : 2.61 % Allowed : 15.89 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2763 helix: 0.03 (0.17), residues: 981 sheet: -0.40 (0.25), residues: 420 loop : -0.67 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 350 HIS 0.008 0.001 HIS C 548 PHE 0.022 0.001 PHE A 357 TYR 0.016 0.001 TYR F 482 ARG 0.004 0.000 ARG D 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 211 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9040 (tt) REVERT: B 513 LYS cc_start: 0.8257 (tptp) cc_final: 0.7954 (tptp) REVERT: C 458 MET cc_start: 0.7872 (tmm) cc_final: 0.7409 (tmm) REVERT: C 480 GLU cc_start: 0.8388 (pt0) cc_final: 0.8116 (pp20) REVERT: D 1 MET cc_start: 0.6750 (tpp) cc_final: 0.6407 (tpp) REVERT: D 554 PHE cc_start: 0.7233 (t80) cc_final: 0.6902 (t80) REVERT: F 42 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7702 (tmm160) REVERT: F 240 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7246 (p90) REVERT: F 481 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7834 (tt) outliers start: 66 outliers final: 48 residues processed: 266 average time/residue: 0.3186 time to fit residues: 138.9764 Evaluate side-chains 248 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 197 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 242 optimal weight: 1.9990 chunk 255 optimal weight: 0.0370 chunk 233 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 108 optimal weight: 0.0770 chunk 195 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 235 optimal weight: 0.0170 chunk 247 optimal weight: 0.7980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 529 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23140 Z= 0.141 Angle : 0.556 10.457 31315 Z= 0.283 Chirality : 0.042 0.198 3540 Planarity : 0.004 0.059 3983 Dihedral : 8.449 164.371 3213 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.73 % Favored : 95.91 % Rotamer: Outliers : 1.55 % Allowed : 17.04 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2763 helix: 0.37 (0.17), residues: 978 sheet: -0.42 (0.25), residues: 422 loop : -0.40 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 350 HIS 0.007 0.001 HIS C 548 PHE 0.027 0.001 PHE E 554 TYR 0.015 0.001 TYR A 670 ARG 0.009 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 513 LYS cc_start: 0.8275 (tptp) cc_final: 0.7981 (tptp) REVERT: B 684 MET cc_start: 0.7623 (tpt) cc_final: 0.6661 (tpt) REVERT: C 458 MET cc_start: 0.7836 (tmm) cc_final: 0.7345 (tmm) REVERT: C 480 GLU cc_start: 0.8212 (pt0) cc_final: 0.7955 (pp20) REVERT: D 1 MET cc_start: 0.6525 (tpp) cc_final: 0.6247 (tpp) REVERT: D 214 MET cc_start: 0.7327 (mtm) cc_final: 0.7067 (mtp) REVERT: D 554 PHE cc_start: 0.7168 (t80) cc_final: 0.6897 (t80) REVERT: E 602 ILE cc_start: 0.9186 (mt) cc_final: 0.8932 (mm) REVERT: F 42 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7805 (tmm160) REVERT: F 174 TYR cc_start: 0.7254 (m-10) cc_final: 0.6849 (m-10) REVERT: F 240 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6964 (p90) outliers start: 39 outliers final: 29 residues processed: 253 average time/residue: 0.3479 time to fit residues: 144.4210 Evaluate side-chains 233 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 163 optimal weight: 7.9990 chunk 263 optimal weight: 0.5980 chunk 160 optimal weight: 0.2980 chunk 124 optimal weight: 0.0000 chunk 182 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 253 optimal weight: 0.0370 chunk 219 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN C 660 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23140 Z= 0.146 Angle : 0.545 10.504 31315 Z= 0.274 Chirality : 0.042 0.175 3540 Planarity : 0.004 0.069 3983 Dihedral : 8.148 161.549 3213 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.66 % Favored : 96.02 % Rotamer: Outliers : 1.35 % Allowed : 17.19 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2763 helix: 0.51 (0.17), residues: 976 sheet: -0.28 (0.25), residues: 423 loop : -0.36 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.007 0.001 HIS C 548 PHE 0.022 0.001 PHE A 357 TYR 0.016 0.001 TYR A 670 ARG 0.003 0.000 ARG D 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 513 LYS cc_start: 0.8243 (tptp) cc_final: 0.7876 (tptp) REVERT: B 684 MET cc_start: 0.7701 (tpt) cc_final: 0.6807 (tpt) REVERT: C 458 MET cc_start: 0.7778 (tmm) cc_final: 0.7297 (tmm) REVERT: C 480 GLU cc_start: 0.8245 (pt0) cc_final: 0.7922 (pp20) REVERT: C 548 HIS cc_start: 0.8861 (t70) cc_final: 0.8427 (t-90) REVERT: D 1 MET cc_start: 0.6436 (tpp) cc_final: 0.5961 (tpp) REVERT: D 214 MET cc_start: 0.7250 (mtm) cc_final: 0.6967 (mtp) REVERT: D 384 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8929 (pp) REVERT: D 463 ASN cc_start: 0.9028 (m110) cc_final: 0.8639 (t0) REVERT: D 554 PHE cc_start: 0.7119 (t80) cc_final: 0.6828 (t80) REVERT: E 575 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7163 (mmtt) REVERT: E 579 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: F 240 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6905 (p90) REVERT: F 481 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7752 (tt) outliers start: 34 outliers final: 28 residues processed: 247 average time/residue: 0.3256 time to fit residues: 131.7264 Evaluate side-chains 242 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 579 GLU Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 174 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.135402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089152 restraints weight = 54503.442| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 4.08 r_work: 0.3197 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23140 Z= 0.187 Angle : 0.562 12.041 31315 Z= 0.282 Chirality : 0.042 0.175 3540 Planarity : 0.004 0.061 3983 Dihedral : 8.071 159.971 3213 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.44 % Rotamer: Outliers : 1.43 % Allowed : 17.47 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2763 helix: 0.47 (0.17), residues: 982 sheet: -0.21 (0.26), residues: 399 loop : -0.37 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 355 HIS 0.007 0.001 HIS C 548 PHE 0.020 0.001 PHE A 357 TYR 0.027 0.001 TYR A 670 ARG 0.005 0.000 ARG F 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4905.18 seconds wall clock time: 91 minutes 4.50 seconds (5464.50 seconds total)